X will gain a new weapon each time you defeat one of the eight bosses. Each weapon has its own special abilities and are certain bosses' weakness, some can also be used to retrieve certain items that are normally out of reach. Zero has his own weapons, but cannot use any of the special weapons X gains.

- X-Buster

The X-Buster is the standard weapon of the game and you begin the game with it. The normal fire will fire the usual standard shot which will cause minimal damage to targets. The charged-up shot will fire a larger beam which causes more damage to targets. Once you find the X-Buster upgrade, X will be able to fire out a wave-type beam and then fire a second shot after the first. If you charge up the X-Buster until X glows red, release the fire button and then quickly fire a second shot which will hit the first one and create a huge blast which causes massive damage to targets.

- Gained from: N/A

- Zero

Zero has two weapons available, his standard Z-Buster, and his Beam Saber. His blaster has the normal firing shot, as well as the charged-up state. To use his triple sabre attack, charge up the weapon until he glows green. When you release the fire button he will fire off one shot and continue to glow green. Fire again and he will shoot another blast. One more time will cause him to take out his Beam Sabre and strike out in front of him at any targets.

- Gained from: N/A

The special weapons can only have their secondary fire mode used when X has the weapon-powerup upgrade and can charge his X-Buster until he glows purple.

- Frost Shield

The Frost Shield is gained once you defeat Blizzard Buffalo. This weapon will fire out a small icicle-type projectile, which will slowly accelerate forward and will strike through any targets. If it hits something and breaks apart, the debris of the projectile will create a small spike object when it hits the ground and will damage anything that touchs them. The charged-up shot will create a large ice block attached to X which can be used to charge against enemies without taking damage.

- Boss: Blizzard Buffalo

- Acid Burst

The Acid Burst is gained once Toxic Seahorse is defeated. This weapon will fire out a small acid bubble which will corrode and damage any target it hits. The bubble will fly out and then land on the ground, spreading out smaller bubbles. The charged-up shot will fire out more than one bubble and will cover a larger area when they hit the ground.

- Boss: Toxic Seahorse

- Tornado Fang

The Tornado Fang is gained once you defeat Tunnel Rhino. This weapon will fire a small drill-projectile which will fly straight ahead and damage any enemies it strikes. This weapon can also be used to destroy crumbling walls found in some stages. The charged-up shot will make a drill appear in front of X and can be used to charge into enemies without taking damage from them. You can also grab onto a wall and stay in position if you activate the secondary fire and jump onto a wall.

- Boss: Tunnel Rhino

- Triad Thunder

The Triad Thunder is gained once Volt Catfish is defeated. This weapon will create three large electric mines around X which will fire out large electric lines to each other and then out in an upward and diagonal directions. The charged-up shot will make X punch the ground and cause everything on the screen to shake. He will then fire out two electric balls either side of him. This technique can be used to destroy some platforms and can destroy the large hanging boulders in Tunnel Rhino's stage.

- Boss: Volt Catfish

- Spinning Blade

The Spinning Blade is gained once you defeat Crush Crawfish. This weapon will fire out two spinning blade projectiles which will fly out from X and then fly back towards him and then behind him. This weapon will take practice to use, but it can be effective for striking high-up targets. The secondary fire will shoot out a large spinning blade attached to X by a long green chain. It will cause heavier damage to targets.

- Boss: Crush Crawfish

- Ray Splasher

The Ray Splasher is gained once Neon Tiger is defeated. This weapon will fire out small rapid energy balls which will fly out on slightly diagonal lines. The secondary fire will cause X to shoot out a crystal ball above him which will randomly fire out small energy balls in different directions, giving him a larger range of fire.

- Boss: Neon Tiger

- Gravity Well

The Gravity Well is gained once you defeat Gravity Beetle. This weapon will fire out a small energy ball which will create a large energy barrier around itself. This weapon will only damage some enemies, and is more effective against some bosses. The secondary fire will shoot a large energy ball straight up and cause all the objects on the screen to fly up. This can be used to raise some platforms in certain stages.

- Boss: Gravity Beetle

- Parasitic Bomb

The Parasitic Bomb is gained once Blast Hornet is defeated. This weapon will fire out a large spike-ball projectile which will trap any enemy it hits. Once the target has been captured, X can walk through them without taking damage. After a few seconds the target will explode. Some enemies will fly around once trapped and fly into other enemies, destroying themself and the other target. The secondary fire will display four cross-hairs around X that will home in one enemies. Once they find a target, a small mechanical bee will fly out of X and slam into the target, destroying it.